The result, coupled with Wisla Krakow's win at Odense, means Fulham must beat the latter in two weeks to be sure of qualification.
Johnson's red card will see him miss that game and Jol admitted the striker's absence is far from ideal.
"It was probably not what you want, a player sent off in the final minutes out of frustration," he said. "It was a second booking, and he knew that he was booked.
"You need all your players, especially Andy Johnson, who has scored goals in Europe.
"He did a very good job for the team. There is no complaint whatsoever with his attitude."